Despite the rapid diversification of morphology and behaviors among pupfish species, gut microbiota related much more closely to the phylogenies of their hosts than to their life history. Reported by the Martin lab (Integrative Biology) in PLOS ONE, September 16, 2022.
Cobamides are important nutrients in microbial communities that can act as public goods, so cobamide availability in a habitat might shape the structure of microbial interactions. New research from the Taga lab characterizes variation in cobamide composition across insect and mammalian guts and environmental samples. Published August 29, 2022 in Biochemistry.
Berkeley scientists contributed to two books this summer on characterizing the structure and importance of microbial communities. Learn how to properly run a microbiome GWAS in Methods in Molecular Biology, or read about soil microbiology in desert ecosystems in Microbiology of Hot Deserts. Congratulations to the Coleman-Derr and Northen groups!
New work from the Banfield lab finds alternative stop codons are widely distributed among phage genomes, including in phages of human and animal gut microbiota. Stop codon has appeared repeatedly in closely related lineages, suggesting it can evolve rapidly. Published May 26, 2022 in Nature Microbiology.
New paper from the Traxler lab describes the discovery of a new family of antimicrobial compounds, referred to as the dynaplanins. The approach took advantage of natural patterns of antimicrobial production and resistance among soil actinomycetes. Published May 24, 2022 in mBio and selected as a 2022 Editor’s Pick.
New work from the Fithian group reports a rarefaction efficiency index to determine the sensitivity of microbiome data to loss upon rarefaction and guide the decisions of researchers. Published February 25, 2022 in Bioinformatics: https://doi.org/10.1093/bioinformatics/btac127.
Announcement of the National Microbiome Data Collaborative Data Portal, a resource for hosting microbiome data that is accessible and usable across systems and studies: https://academic.oup.com/nar/article/50/D1/D828/6414581
The Yoshikuni group (Lawrence Berkeley Lab) integrates chassis-independent recombinase-assisted genome engineering with CRISPR to rapidly profile the function of bacterial biosynthetic gene clusters. Published September 10th, 2021 in Cell Chemical Biology: https://doi.org/10.1016/j.chembiol.2021.08.009
Congratulations to the Banfield Lab (Environmental Science, Policy, and Management) for two new publications describing the diversity and metabolic capabilities of the largely uncultivated, ultra-small bacteria comprising the Candidate Phyla Radiation. Published July 13th, 2021 and August 17th, 2021 in mSystems: https://doi.org/10.1128/mBio.00521-21, https://doi.org/10.1128/mSystems.01205-20
A large-scale field experiment from the Firestone lab (Environmental Science, Policy, and Management) shows that distinct protist communities inhabit the rhizosphere in different plant developmental stages, shedding new light on an understudied component of the plant microbiome. Published April 28, 2021 in Microbiome: https://doi.org/10.1186/s40168-021-01042-9
New pipeline developed by Jan-Feng Cheng (Joint Genome Institute) and colleagues for single-cell sequencing of microbial eukaryotes. Published April 23, 2021 in iScience: https://www.cell.com/iscience/pdf/S2589-0042(21)00258-3.pdf
The Zhang lab (Chemical and Biomolecular Engineering) identified biochemical mechanisms of adhesion and biofilm formations in Streptococcus mutans, a significant contributor to tooth decay in the human oral microbiota. Published March 4, 2021 in Nature Chemical Biology: https://doi.org/10.1038/s41589-021-00745-2